Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Hela cells
cell line
HeLa
chip antibody
H3K4me3 (in-house EDL Lot 1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin input was prepeared by the combination of MNase treatment and sonication, and the chromatin associated with histone modification was isolated using indicated antibody. Libraries were prepared using ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to the manufacturer’s instructions. The adapter-ligated DNA was PCR amplified for 12 cycles.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
29818138
Reads aligned (%)
98.7
Duplicates removed (%)
8.0
Number of peaks
22955 (qval < 1E-05)

hg19

Number of total reads
29818138
Reads aligned (%)
97.6
Duplicates removed (%)
8.9
Number of peaks
22538 (qval < 1E-05)

Base call quality data from DBCLS SRA